Reading the literature on any neurodegenerative condition quickly leads to a bewildering array of facts, some contradictory, regarding the correlations between known pathological and clinical features of the disease. To help unravel the multifaceted dimensions of diseases such as Parkinsonian disorders and cerebral ischemia, we describe a formal system for representing the characteristics of human neurological disease and animal models to promote understanding of disease mechanisms and to provide a more rigorous method to compare model systems and human disease. This collaboration between the National Center for Biomedical Ontologies (NCBO), the National Center for Microscopy and Imaging Research and the Biomedical Informatics Research Network project will develop tools that bridge between information contained in ontologies, distributed databases and images. This work builds upon efforts at NCBO to develop a Phenotype and Trait Ontology for expression of complex phenotypes in a machine-processable form, so that powerful algorithms can be employed to look for correlations and interesting patterns in the data. Ontologies for annotation of complex traits from animal models of Parkinsonian disorders and transient cerebral ischemia will be developed and applied to an analysis of multiscale imaging data. This ontology will provide the means to perform ontology-based image analysis and correlation of phenotypes across scales. This project forms a driving biological project for NCBO, bringing the need for ontology-based analysis of multiple spatial and temporal scales into the frameworks under development at NCBO, while at the same time contributing ontologies and data into the Open Biological Ontologies and Data repositories curated by NCBO. A core component of the proposal is the development of an integrated ontology-based environment for the that will help the scientist to understand the deep interrelationships among observed data and collected knowledge about neurological diseases such as Parkinson's. The proposed work thus aligns directly with the stated objectives of NCBO: create, access and browse relevant ontologies;use ontologies to annotate experimental datasets;access and draw inferences from the annotated data;and bridge between model systems and human disease. Eventhough tools developed as part of this proposal will be developed in the context of a specific driving biological project they will be broadly applicable to other imaging